7CTH | pdb_00007cth

Cryo-EM structure of dengue virus serotype 2 in complex with the scFv fragment of the broadly neutralizing antibody EDE1 C10


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7CTH

This is version 1.3 of the entry. See complete history

Literature

The epitope arrangement on flavivirus particles contributes to Mab C10's extraordinary neutralization breadth across Zika and dengue viruses.

Sharma, A.Zhang, X.Dejnirattisai, W.Dai, X.Gong, D.Wongwiwat, W.Duquerroy, S.Rouvinski, A.Vaney, M.C.Guardado-Calvo, P.Haouz, A.England, P.Sun, R.Zhou, Z.H.Mongkolsapaya, J.Screaton, G.R.Rey, F.A.

(2021) Cell 184: 6052

  • DOI: https://doi.org/10.1016/j.cell.2021.11.010
  • Primary Citation Related Structures: 
    7A3N, 7A3O, 7A3P, 7A3Q, 7A3R, 7A3S, 7A3T, 7A3U, 7CTH

  • PubMed Abstract: 

    The human monoclonal antibody C10 exhibits extraordinary cross-reactivity, potently neutralizing Zika virus (ZIKV) and the four serotypes of dengue virus (DENV1-DENV4). Here we describe a comparative structure-function analysis of C10 bound to the envelope (E) protein dimers of the five viruses it neutralizes. We demonstrate that the C10 Fab has high affinity for ZIKV and DENV1 but not for DENV2, DENV3, and DENV4. We further show that the C10 interaction with the latter viruses requires an E protein conformational landscape that limits binding to only one of the three independent epitopes per virion. This limited affinity is nevertheless counterbalanced by the particle's icosahedral organization, which allows two different dimers to be reached by both Fab arms of a C10 immunoglobulin. The epitopes' geometric distribution thus confers C10 its exceptional neutralization breadth. Our results highlight the importance not only of paratope/epitope complementarity but also the topological distribution for epitope-focused vaccine design.


  • Organizational Affiliation
    • Institut Pasteur, Université de Paris, CNRS UMR3569, Unité de Virologie Structurale, 75015 Paris, France.

Macromolecule Content 

  • Total Structure Weight: 251.6 kDa 
  • Atom Count: 16,667 
  • Modeled Residue Count: 2,157 
  • Deposited Residue Count: 2,306 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Core protein
A, B, C
495dengue virus type 2Mutation(s): 0 
UniProt
Find proteins for P14340 (Dengue virus type 2 (strain Thailand/NGS-C/1944))
Explore P14340 
Go to UniProtKB:  P14340
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14340
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Core proteinD [auth F],
E [auth D],
F [auth E]
75dengue virus type 2Mutation(s): 0 
Gene Names: POLY
EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt
Find proteins for P14340 (Dengue virus type 2 (strain Thailand/NGS-C/1944))
Explore P14340 
Go to UniProtKB:  P14340
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14340
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Single Chain Variable FragmentG [auth I],
I [auth H]
144Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Single Chain Variable FragmentH [auth M],
J [auth L]
154Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcisTEM

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustFrance--
National Natural Science Foundation of China (NSFC)China31600606
National Basic Research Program of China (973 Program)China2016YFA0501100

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-01
    Type: Initial release
  • Version 1.1: 2021-12-08
    Changes: Database references
  • Version 1.2: 2022-02-16
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-10-30
    Changes: Data collection, Structure summary